PHENOMS documentation#

PHENOMS (Python-based Hydrogen-Deuterium Exchange of Molecular Dynamics Simulations) quantifies local H-bond networks from MD trajectories to support HDX-MS–style interpretation—signals that global metrics like RMSD/RMSF often miss.

What you get#

Baker–Hubbard H-bond detection with an optional Rust kernel (~17–24× vs common Python backends in our 4-CPU Docker benchmark)
Backbone N–O mode by default (HDX-relevant); opt into all donor/acceptor classes
Replicate-aware workflows via SimulationSet and ComparisonSet
Inputs: multi-frame PDBs, native traj+topology, or engine folders (GROMACS / OpenMM / AMBER)
Exports: occupancy CSVs, heatmaps, differential protection, connectivity graphs, PDB B-factors
Optional CLI (phenoms) wrapping the same Python API

At a glance#

from phenoms import SimulationSet

sim = SimulationSet(
    pdb_files=["rep1.pdb", "rep2.pdb"],
    sub_frames=100,
    backbone_only=True,  # default
)
sim.run()

Contents

Installation
Usage
Command-line interface
Outputs
Benchmarks
API reference